RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 04-Jul-2021 01:18:12 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/2_msa/Q14692_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692 --seed 2 --threads 8 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (8 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/2_msa/Q14692_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 831 sites WARNING: Sequences tr_B6Q752_B6Q752_TALMQ_441960 and tr_A0A093VGY9_A0A093VGY9_TALMA_1077442 are exactly identical! WARNING: Sequences tr_Q29EX5_Q29EX5_DROPS_46245 and tr_B4H5N4_B4H5N4_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NGP3_B8NGP3_ASPFN_332952 and tr_Q2UFC8_Q2UFC8_ASPOR_510516 are exactly identical! WARNING: Sequences tr_A0A179UGI5_A0A179UGI5_BLAGS_559298 and tr_C5GT24_C5GT24_AJEDR_559297 are exactly identical! WARNING: Sequences tr_C6HE12_C6HE12_AJECH_544712 and tr_F0UUP6_F0UUP6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0GLY8_A0A0E0GLY8_ORYNI_4536 and tr_A0A0E0NUL3_A0A0E0NUL3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2QD31_A2QD31_ASPNC_425011 and tr_G3Y395_G3Y395_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QD31_A2QD31_ASPNC_425011 and tr_A0A319B8N3_A0A319B8N3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X507_G7X507_ASPKW_1033177 and tr_A0A146FND2_A0A146FND2_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2YQ36_G2YQ36_BOTF4_999810 and tr_M7TW87_M7TW87_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A0D2XWA0_A0A0D2XWA0_FUSO4_426428 and tr_X0BSI0_X0BSI0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XWA0_A0A0D2XWA0_FUSO4_426428 and tr_A0A2H3TTC0_A0A2H3TTC0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W2PSB1_W2PSB1_PHYPN_761204 and tr_W2G8B2_W2G8B2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0F0HYL3_A0A0F0HYL3_ASPPU_1403190 and tr_A0A2G7FLU0_A0A2G7FLU0_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8V9Y8_A0A0F8V9Y8_9EURO_308745 and tr_A0A2T5LTM7_A0A2T5LTM7_9EURO_1392256 are exactly identical! WARNING: Duplicate sequences found: 15 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.reduced.phy Alignment comprises 1 partitions and 831 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 831 / 831 Gaps: 8.18 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.rba Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 208 / 16640 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -1058535.797902] Initial branch length optimization [00:00:06 -915533.628087] Model parameter optimization (eps = 10.000000) [00:01:01 -911473.737650] AUTODETECT spr round 1 (radius: 5) [00:04:03 -648755.011605] AUTODETECT spr round 2 (radius: 10) [00:07:13 -468625.938172] AUTODETECT spr round 3 (radius: 15) [00:10:47 -383093.939152] AUTODETECT spr round 4 (radius: 20) [00:14:48 -366814.182627] AUTODETECT spr round 5 (radius: 25) [00:18:46 -364405.529361] SPR radius for FAST iterations: 25 (autodetect) [00:18:46 -364405.529361] Model parameter optimization (eps = 3.000000) [00:19:10 -364056.696082] FAST spr round 1 (radius: 25) [00:23:00 -319794.609551] FAST spr round 2 (radius: 25) [00:25:56 -317914.079690] FAST spr round 3 (radius: 25) [00:28:21 -317871.995976] FAST spr round 4 (radius: 25) [00:30:30 -317863.458324] FAST spr round 5 (radius: 25) [00:32:33 -317862.185446] FAST spr round 6 (radius: 25) [00:34:32 -317860.150342] FAST spr round 7 (radius: 25) [00:36:31 -317857.783559] FAST spr round 8 (radius: 25) [00:38:27 -317857.783431] Model parameter optimization (eps = 1.000000) [00:38:44 -317845.686886] SLOW spr round 1 (radius: 5) [00:41:43 -317767.075126] SLOW spr round 2 (radius: 5) [00:44:36 -317759.161494] SLOW spr round 3 (radius: 5) [00:47:21 -317756.680948] SLOW spr round 4 (radius: 5) [00:50:03 -317756.680572] SLOW spr round 5 (radius: 10) [00:52:56 -317754.310062] SLOW spr round 6 (radius: 5) [00:56:29 -317754.297718] SLOW spr round 7 (radius: 10) [00:59:43 -317754.297481] SLOW spr round 8 (radius: 15) [01:04:18 -317754.297245] SLOW spr round 9 (radius: 20) [01:11:56 -317754.297008] SLOW spr round 10 (radius: 25) [01:20:42] [worker #1] ML tree search #2, logLikelihood: -317757.504683 [01:21:08 -317754.296770] Model parameter optimization (eps = 0.100000) [01:21:17] [worker #0] ML tree search #1, logLikelihood: -317754.192322 [01:21:17 -1061320.149660] Initial branch length optimization [01:21:24 -917965.257790] Model parameter optimization (eps = 10.000000) [01:22:12 -913779.759361] AUTODETECT spr round 1 (radius: 5) [01:25:18 -648790.619009] AUTODETECT spr round 2 (radius: 10) [01:28:30 -484995.211226] AUTODETECT spr round 3 (radius: 15) [01:32:06 -413020.860394] AUTODETECT spr round 4 (radius: 20) [01:35:59 -399051.798760] AUTODETECT spr round 5 (radius: 25) [01:40:20 -393427.417095] SPR radius for FAST iterations: 25 (autodetect) [01:40:20 -393427.417095] Model parameter optimization (eps = 3.000000) [01:40:45 -393050.955936] FAST spr round 1 (radius: 25) [01:44:40 -324183.093714] FAST spr round 2 (radius: 25) [01:47:41 -318229.717561] FAST spr round 3 (radius: 25) [01:50:14 -317918.584934] FAST spr round 4 (radius: 25) [01:52:30 -317887.412656] FAST spr round 5 (radius: 25) [01:54:33 -317887.372593] Model parameter optimization (eps = 1.000000) [01:54:50 -317876.759322] SLOW spr round 1 (radius: 5) [01:57:53 -317795.032990] SLOW spr round 2 (radius: 5) [02:00:45 -317789.486797] SLOW spr round 3 (radius: 5) [02:03:28 -317784.898558] SLOW spr round 4 (radius: 5) [02:06:10 -317784.898341] SLOW spr round 5 (radius: 10) [02:09:02 -317784.898178] SLOW spr round 6 (radius: 15) [02:13:45 -317784.898035] SLOW spr round 7 (radius: 20) [02:20:35 -317784.897901] SLOW spr round 8 (radius: 25) [02:29:34 -317784.897771] Model parameter optimization (eps = 0.100000) [02:29:44] [worker #0] ML tree search #3, logLikelihood: -317784.702474 [02:29:45 -1059580.910393] Initial branch length optimization [02:29:52 -915354.076001] Model parameter optimization (eps = 10.000000) [02:30:39 -911055.433070] AUTODETECT spr round 1 (radius: 5) [02:33:42 -635910.075107] AUTODETECT spr round 2 (radius: 10) [02:36:49 -459423.702263] AUTODETECT spr round 3 (radius: 15) [02:40:19 -386794.520085] AUTODETECT spr round 4 (radius: 20) [02:44:38 -365045.459015] AUTODETECT spr round 5 (radius: 25) [02:49:11 -363713.851354] SPR radius for FAST iterations: 25 (autodetect) [02:49:11 -363713.851354] Model parameter optimization (eps = 3.000000) [02:49:33 -363400.135556] FAST spr round 1 (radius: 25) [02:53:19 -319793.555510] FAST spr round 2 (radius: 25) [02:56:10] [worker #1] ML tree search #4, logLikelihood: -317757.299338 [02:56:17 -317999.570307] FAST spr round 3 (radius: 25) [02:58:50 -317867.469087] FAST spr round 4 (radius: 25) [03:00:57 -317853.125437] FAST spr round 5 (radius: 25) [03:03:00 -317850.092235] FAST spr round 6 (radius: 25) [03:04:59 -317850.092103] Model parameter optimization (eps = 1.000000) [03:05:07 -317848.582229] SLOW spr round 1 (radius: 5) [03:08:14 -317765.893111] SLOW spr round 2 (radius: 5) [03:11:07 -317762.030084] SLOW spr round 3 (radius: 5) [03:13:51 -317762.029477] SLOW spr round 4 (radius: 10) [03:16:42 -317761.820560] SLOW spr round 5 (radius: 5) [03:20:15 -317761.820302] SLOW spr round 6 (radius: 10) [03:23:30 -317761.820060] SLOW spr round 7 (radius: 15) [03:28:06 -317761.819817] SLOW spr round 8 (radius: 20) [03:35:24 -317761.819574] SLOW spr round 9 (radius: 25) [03:44:52 -317761.819330] Model parameter optimization (eps = 0.100000) [03:45:01] [worker #0] ML tree search #5, logLikelihood: -317760.945497 [03:45:01 -1057795.446304] Initial branch length optimization [03:45:08 -914161.843672] Model parameter optimization (eps = 10.000000) [03:46:27 -910156.788051] AUTODETECT spr round 1 (radius: 5) [03:49:25 -654353.839594] AUTODETECT spr round 2 (radius: 10) [03:52:36 -463331.484913] AUTODETECT spr round 3 (radius: 15) [03:56:13 -378412.739526] AUTODETECT spr round 4 (radius: 20) [04:00:21 -362559.249737] AUTODETECT spr round 5 (radius: 25) [04:05:15 -361001.000732] SPR radius for FAST iterations: 25 (autodetect) [04:05:15 -361001.000732] Model parameter optimization (eps = 3.000000) [04:05:42 -360675.495374] FAST spr round 1 (radius: 25) [04:09:28 -318877.352254] FAST spr round 2 (radius: 25) [04:12:18 -317877.102845] FAST spr round 3 (radius: 25) [04:14:41 -317830.001300] FAST spr round 4 (radius: 25) [04:16:51 -317813.024306] FAST spr round 5 (radius: 25) [04:17:06] [worker #1] ML tree search #6, logLikelihood: -317768.855151 [04:18:52 -317813.023213] Model parameter optimization (eps = 1.000000) [04:19:04 -317811.108283] SLOW spr round 1 (radius: 5) [04:22:04 -317751.888379] SLOW spr round 2 (radius: 5) [04:24:55 -317750.412757] SLOW spr round 3 (radius: 5) [04:27:39 -317750.412339] SLOW spr round 4 (radius: 10) [04:30:32 -317750.412097] SLOW spr round 5 (radius: 15) [04:35:26 -317750.411867] SLOW spr round 6 (radius: 20) [04:42:52 -317748.636066] SLOW spr round 7 (radius: 5) [04:46:47 -317747.330580] SLOW spr round 8 (radius: 5) [04:50:03 -317747.330231] SLOW spr round 9 (radius: 10) [04:53:07 -317747.329997] SLOW spr round 10 (radius: 15) [04:57:47 -317747.329765] SLOW spr round 11 (radius: 20) [05:05:10 -317747.329533] SLOW spr round 12 (radius: 25) [05:14:46 -317747.329301] Model parameter optimization (eps = 0.100000) [05:14:55] [worker #0] ML tree search #7, logLikelihood: -317747.186298 [05:14:55 -1059098.851352] Initial branch length optimization [05:15:02 -917145.240280] Model parameter optimization (eps = 10.000000) [05:16:02 -913004.309005] AUTODETECT spr round 1 (radius: 5) [05:19:03 -635714.377085] AUTODETECT spr round 2 (radius: 10) [05:22:14 -472425.650571] AUTODETECT spr round 3 (radius: 15) [05:25:45 -387722.020696] AUTODETECT spr round 4 (radius: 20) [05:30:03 -363109.990774] AUTODETECT spr round 5 (radius: 25) [05:35:00 -360508.282314] SPR radius for FAST iterations: 25 (autodetect) [05:35:00 -360508.282314] Model parameter optimization (eps = 3.000000) [05:35:09 -360503.473742] FAST spr round 1 (radius: 25) [05:38:53 -319348.164183] FAST spr round 2 (radius: 25) [05:41:48 -318230.904432] FAST spr round 3 (radius: 25) [05:44:12 -318178.227267] FAST spr round 4 (radius: 25) [05:46:22 -318160.578830] FAST spr round 5 (radius: 25) [05:47:25] [worker #1] ML tree search #8, logLikelihood: -317749.848504 [05:48:24 -318155.624742] FAST spr round 6 (radius: 25) [05:50:23 -318155.624612] Model parameter optimization (eps = 1.000000) [05:50:43 -317884.904063] SLOW spr round 1 (radius: 5) [05:53:48 -317787.352480] SLOW spr round 2 (radius: 5) [05:56:40 -317783.356093] SLOW spr round 3 (radius: 5) [05:59:24 -317783.141289] SLOW spr round 4 (radius: 5) [06:02:07 -317783.140965] SLOW spr round 5 (radius: 10) [06:04:59 -317783.140733] SLOW spr round 6 (radius: 15) [06:09:51 -317783.140501] SLOW spr round 7 (radius: 20) [06:16:49 -317781.369369] SLOW spr round 8 (radius: 5) [06:20:42 -317780.071203] SLOW spr round 9 (radius: 5) [06:24:00 -317780.070798] SLOW spr round 10 (radius: 10) [06:27:04 -317780.070559] SLOW spr round 11 (radius: 15) [06:31:42 -317780.070324] SLOW spr round 12 (radius: 20) [06:38:40 -317780.070089] SLOW spr round 13 (radius: 25) [06:47:45 -317780.069854] Model parameter optimization (eps = 0.100000) [06:47:55] [worker #0] ML tree search #9, logLikelihood: -317779.811665 [06:47:55 -1058092.490769] Initial branch length optimization [06:48:02 -915796.449471] Model parameter optimization (eps = 10.000000) [06:49:16 -911672.122531] AUTODETECT spr round 1 (radius: 5) [06:52:18 -624510.119338] AUTODETECT spr round 2 (radius: 10) [06:55:28 -445310.180569] AUTODETECT spr round 3 (radius: 15) [06:58:54 -391745.660122] AUTODETECT spr round 4 (radius: 20) [07:03:15 -367200.571214] AUTODETECT spr round 5 (radius: 25) [07:08:27 -364581.664240] SPR radius for FAST iterations: 25 (autodetect) [07:08:27 -364581.664240] Model parameter optimization (eps = 3.000000) [07:08:52 -364295.859025] FAST spr round 1 (radius: 25) [07:12:48 -319254.144797] FAST spr round 2 (radius: 25) [07:15:40 -317965.447153] FAST spr round 3 (radius: 25) [07:18:06 -317886.102559] FAST spr round 4 (radius: 25) [07:19:55] [worker #1] ML tree search #10, logLikelihood: -317745.113673 [07:20:11 -317884.197572] FAST spr round 5 (radius: 25) [07:22:13 -317884.197337] Model parameter optimization (eps = 1.000000) [07:22:27 -317880.344892] SLOW spr round 1 (radius: 5) [07:25:36 -317800.411310] SLOW spr round 2 (radius: 5) [07:28:31 -317782.776592] SLOW spr round 3 (radius: 5) [07:31:15 -317782.368822] SLOW spr round 4 (radius: 5) [07:33:56 -317782.368590] SLOW spr round 5 (radius: 10) [07:36:49 -317782.368365] SLOW spr round 6 (radius: 15) [07:41:33 -317782.368139] SLOW spr round 7 (radius: 20) [07:48:35 -317782.367913] SLOW spr round 8 (radius: 25) [07:57:56 -317782.367687] Model parameter optimization (eps = 0.100000) [07:58:02] [worker #0] ML tree search #11, logLikelihood: -317782.313314 [07:58:02 -1058231.536898] Initial branch length optimization [07:58:09 -914681.959351] Model parameter optimization (eps = 10.000000) [07:59:04 -910521.415215] AUTODETECT spr round 1 (radius: 5) [08:02:08 -641835.984977] AUTODETECT spr round 2 (radius: 10) [08:05:16 -473746.864114] AUTODETECT spr round 3 (radius: 15) [08:08:48 -419564.795103] AUTODETECT spr round 4 (radius: 20) [08:12:51 -379621.520741] AUTODETECT spr round 5 (radius: 25) [08:17:58 -369160.036345] SPR radius for FAST iterations: 25 (autodetect) [08:17:58 -369160.036345] Model parameter optimization (eps = 3.000000) [08:18:25 -368852.039977] FAST spr round 1 (radius: 25) [08:22:12 -320024.563665] FAST spr round 2 (radius: 25) [08:24:56 -318050.293459] FAST spr round 3 (radius: 25) [08:27:20 -317878.115290] FAST spr round 4 (radius: 25) [08:29:29 -317873.513652] FAST spr round 5 (radius: 25) [08:31:28 -317873.513256] Model parameter optimization (eps = 1.000000) [08:31:40 -317871.684565] SLOW spr round 1 (radius: 5) [08:34:40 -317786.295442] SLOW spr round 2 (radius: 5) [08:37:30 -317776.544781] SLOW spr round 3 (radius: 5) [08:40:15] [worker #1] ML tree search #12, logLikelihood: -317753.485929 [08:40:15 -317764.559651] SLOW spr round 4 (radius: 5) [08:42:59 -317764.559397] SLOW spr round 5 (radius: 10) [08:45:54 -317759.775829] SLOW spr round 6 (radius: 5) [08:49:29 -317757.822768] SLOW spr round 7 (radius: 5) [08:52:35 -317757.822527] SLOW spr round 8 (radius: 10) [08:55:34 -317757.590837] SLOW spr round 9 (radius: 5) [08:59:08 -317754.808343] SLOW spr round 10 (radius: 5) [09:02:12 -317754.808119] SLOW spr round 11 (radius: 10) [09:05:11 -317754.807897] SLOW spr round 12 (radius: 15) [09:09:56 -317754.807675] SLOW spr round 13 (radius: 20) [09:17:04 -317754.807452] SLOW spr round 14 (radius: 25) [09:26:16 -317754.807229] Model parameter optimization (eps = 0.100000) [09:26:28] [worker #0] ML tree search #13, logLikelihood: -317754.624375 [09:26:28 -1053917.665881] Initial branch length optimization [09:26:34 -910796.442741] Model parameter optimization (eps = 10.000000) [09:27:20 -906659.591604] AUTODETECT spr round 1 (radius: 5) [09:30:21 -659939.016570] AUTODETECT spr round 2 (radius: 10) [09:33:30 -492186.904333] AUTODETECT spr round 3 (radius: 15) [09:37:11 -410213.595054] AUTODETECT spr round 4 (radius: 20) [09:41:09 -377378.262500] AUTODETECT spr round 5 (radius: 25) [09:45:23 -372978.017194] SPR radius for FAST iterations: 25 (autodetect) [09:45:23 -372978.017194] Model parameter optimization (eps = 3.000000) [09:45:45 -372655.358360] FAST spr round 1 (radius: 25) [09:48:48] [worker #1] ML tree search #14, logLikelihood: -317768.452518 [09:49:38 -320241.858678] FAST spr round 2 (radius: 25) [09:52:29 -317955.152331] FAST spr round 3 (radius: 25) [09:54:58 -317862.207115] FAST spr round 4 (radius: 25) [09:57:09 -317845.115074] FAST spr round 5 (radius: 25) [09:59:13 -317843.578745] FAST spr round 6 (radius: 25) [10:01:13 -317842.835469] FAST spr round 7 (radius: 25) [10:03:12 -317842.834857] Model parameter optimization (eps = 1.000000) [10:03:24 -317840.938228] SLOW spr round 1 (radius: 5) [10:06:28 -317756.277152] SLOW spr round 2 (radius: 5) [10:09:19 -317748.146216] SLOW spr round 3 (radius: 5) [10:12:03 -317747.000301] SLOW spr round 4 (radius: 5) [10:14:45 -317747.000172] SLOW spr round 5 (radius: 10) [10:17:41 -317746.475676] SLOW spr round 6 (radius: 5) [10:21:15 -317746.306376] SLOW spr round 7 (radius: 5) [10:24:21 -317746.304847] SLOW spr round 8 (radius: 10) [10:27:21 -317745.642119] SLOW spr round 9 (radius: 5) [10:30:51 -317745.634278] SLOW spr round 10 (radius: 10) [10:34:01 -317745.632826] SLOW spr round 11 (radius: 15) [10:38:31 -317745.632274] SLOW spr round 12 (radius: 20) [10:45:35 -317745.632011] SLOW spr round 13 (radius: 25) [10:54:50 -317745.631842] Model parameter optimization (eps = 0.100000) [10:54:59] [worker #0] ML tree search #15, logLikelihood: -317745.475639 [10:54:59 -1060332.383487] Initial branch length optimization [10:55:06 -918836.456118] Model parameter optimization (eps = 10.000000) [10:55:48 -914889.841634] AUTODETECT spr round 1 (radius: 5) [10:58:49 -642511.775901] AUTODETECT spr round 2 (radius: 10) [11:01:59 -473980.641812] AUTODETECT spr round 3 (radius: 15) [11:05:24] [worker #1] ML tree search #16, logLikelihood: -317752.746225 [11:05:29 -415471.043542] AUTODETECT spr round 4 (radius: 20) [11:09:25 -378382.114127] AUTODETECT spr round 5 (radius: 25) [11:13:57 -373892.062902] SPR radius for FAST iterations: 25 (autodetect) [11:13:57 -373892.062902] Model parameter optimization (eps = 3.000000) [11:14:20 -373557.661168] FAST spr round 1 (radius: 25) [11:18:10 -319561.808193] FAST spr round 2 (radius: 25) [11:21:07 -317971.159502] FAST spr round 3 (radius: 25) [11:23:39 -317878.085806] FAST spr round 4 (radius: 25) [11:25:56 -317858.633961] FAST spr round 5 (radius: 25) [11:28:02 -317857.244763] FAST spr round 6 (radius: 25) [11:30:02 -317857.244506] Model parameter optimization (eps = 1.000000) [11:30:18 -317851.699995] SLOW spr round 1 (radius: 5) [11:33:24 -317771.211007] SLOW spr round 2 (radius: 5) [11:36:20 -317764.629743] SLOW spr round 3 (radius: 5) [11:39:08 -317762.091959] SLOW spr round 4 (radius: 5) [11:41:51 -317762.091792] SLOW spr round 5 (radius: 10) [11:44:46 -317761.371980] SLOW spr round 6 (radius: 5) [11:48:21 -317761.371816] SLOW spr round 7 (radius: 10) [11:51:38 -317761.073357] SLOW spr round 8 (radius: 5) [11:55:05 -317761.073153] SLOW spr round 9 (radius: 10) [11:58:18 -317761.073032] SLOW spr round 10 (radius: 15) [12:02:57 -317761.072916] SLOW spr round 11 (radius: 20) [12:10:22 -317761.072801] SLOW spr round 12 (radius: 25) [12:19:51 -317761.072686] Model parameter optimization (eps = 0.100000) [12:19:57] [worker #0] ML tree search #17, logLikelihood: -317761.041375 [12:19:58 -1058140.099503] Initial branch length optimization [12:20:04 -917014.621377] Model parameter optimization (eps = 10.000000) [12:21:08 -912971.492288] AUTODETECT spr round 1 (radius: 5) [12:24:23 -639927.631754] AUTODETECT spr round 2 (radius: 10) [12:27:17] [worker #1] ML tree search #18, logLikelihood: -317745.643229 [12:27:43 -455274.985195] AUTODETECT spr round 3 (radius: 15) [12:31:36 -385048.403074] AUTODETECT spr round 4 (radius: 20) [12:35:58 -367406.654700] AUTODETECT spr round 5 (radius: 25) [12:41:43 -365381.946156] SPR radius for FAST iterations: 25 (autodetect) [12:41:43 -365381.946156] Model parameter optimization (eps = 3.000000) [12:42:15 -365035.212916] FAST spr round 1 (radius: 25) [12:46:28 -319123.707677] FAST spr round 2 (radius: 25) [12:49:30 -317992.882557] FAST spr round 3 (radius: 25) [12:52:10 -317888.621783] FAST spr round 4 (radius: 25) [12:54:42 -317872.902221] FAST spr round 5 (radius: 25) [12:56:53 -317872.270240] FAST spr round 6 (radius: 25) [12:59:00 -317872.270173] Model parameter optimization (eps = 1.000000) [12:59:19 -317857.423806] SLOW spr round 1 (radius: 5) [13:02:34 -317760.059031] SLOW spr round 2 (radius: 5) [13:05:38 -317756.903784] SLOW spr round 3 (radius: 5) [13:08:33 -317755.702080] SLOW spr round 4 (radius: 5) [13:11:26 -317755.701945] SLOW spr round 5 (radius: 10) [13:14:19 -317755.388688] SLOW spr round 6 (radius: 5) [13:17:51 -317755.262296] SLOW spr round 7 (radius: 5) [13:20:55 -317755.260391] SLOW spr round 8 (radius: 10) [13:23:56 -317755.260266] SLOW spr round 9 (radius: 15) [13:28:48 -317755.260202] SLOW spr round 10 (radius: 20) [13:35:35 -317755.260140] SLOW spr round 11 (radius: 25) [13:44:19 -317755.260077] Model parameter optimization (eps = 0.100000) [13:44:25] [worker #0] ML tree search #19, logLikelihood: -317755.199595 [14:01:37] [worker #1] ML tree search #20, logLikelihood: -317759.782623 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.208004,0.428293) (0.324102,0.581520) (0.277136,0.982336) (0.190758,2.360058) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Final LogLikelihood: -317745.113673 AIC score: 639500.227346 / AICc score: 8683560.227346 / BIC score: 648969.100085 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=831). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 38 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14692/3_mltree/Q14692.raxml.log Analysis started: 04-Jul-2021 01:18:12 / finished: 04-Jul-2021 15:19:50 Elapsed time: 50497.819 seconds Consumed energy: 4469.268 Wh (= 22 km in an electric car, or 112 km with an e-scooter!)